On 10/06/2014 10:29 AM, Daniel Schmolze wrote:
Thanks Martin, that makes sense. I think your suggestion may be my only option.
I hope by 'my suggestion' you mean contacting the survcomp maintainer(s) (I have
bcc'd them on this email) and letting them know!
Martin
On Mon, Oct 6, 2014 at 1:19 PM, Martin Morgan <mtmor...@fhcrc.org> wrote:
On 10/06/2014 07:52 AM, Daniel Schmolze wrote:
I'm getting a vignette error from the BioC build servers that I can't
reproduce locally:
* creating vignettes ... ERROR
Quitting from lines 116-119 (saps.Rmd)
Error: processing vignette 'saps.Rmd' failed with diagnostics:
could not find function "survfit"
The offending lines in saps.Rmd call a function in my package,
plotKM(), which in turn calls makes the following call:
survcomp::km.coxph.plot(
formula.s = survival::Surv(survivalTimes, followup) ~ cluster,
data.s = dd, main.title=title, y.label=y.label, x.label=x.label,
o.text=text, ...)
survfit() is part of the "survival" package, and nowhere is it
explicitly called, but I suppose it's being called from within
km.coxph.plot()? My package imports both the "survival" and "survcomp"
packages in the DESCRIPTION file.
Hi Daniel --
if it's being called by km.coxph.plot, then the problem is with survcomp,
which from this line
getNamespaceImports("survcomp")$survival
survivalROC survivalROC.C
"survivalROC" "survivalROC.C"
is failing to import(survival, survfit). The survcomp author needs to update
their package; you could add survival to your Depends: field, but there are
then circumstances when your package would not work (e.g., when the next guy
down Imports: or Depends: on your package).
Martin
R CMD check, R CMD check --as-cran, and R CMD BiocCheck all work fine
on several different computers for me. Any ideas?
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PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
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